 GEP Digital Laboratory Notebook Nick Reeves, Mt. San Jacinto Community College

Claiming and Delivering Files and Projects  I claimed lower difficulty contigs (level 4 or 5) with 2 genes identified by the BLASTX evidence track  All files were delivered to student computers through the course Blackboard website and the Dropbox file sharing program which worked but was a little clunky… Google docs may be a better delivery method

DLN Page 1 - Synteny  Basic synteny analysis that compares the query genome to the reference D. melanogaster genome  Aligns well with basic chromosome concepts covered in class – loci/linkage/cell division  Introduces students to the GEP genome browser and Flybase gbrowse

DLN Page 2 – Gene Structure  Pick one of the two genes in the contig and compare the gene structure of the query BLASTX track and the reference D. melanogaster annotation  Emphasize  Number of isoforms  Number of exons  Alternative splicing  Open reading frame  Not considering the sequence yet

DLN Page 3 – Coding DNA Sequence  The actual CDS annotation!  Important coordinates in yellow box. Several pages long…  Start at the start codon – It’s painted green!  Watch what strand is being analyzed!  Reveals student misconceptions - UTRs  Synthesis of evidence  BLAST track finds homologs  Gene predictions indicate boundaries  RNA-seq shows expression and verifies boundaries  Gene Record Finder for amino acid sequence – students identify the matching amino acids

Gene Record Finder

DLN Page 3 – Coding DNA Sequence  Intron boundaries defined by splice site consensus sequence AG/GT and synthesis of evidence tracks  Frame vs. phase – critical thinking! A practice activity would be helpful.

DLN Page 3 – Coding DNA Sequence  Intron boundaries defined by splice site consensus sequence AG/GT and synthesis of evidence tracks  Frame vs. phase – critical thinking! A practice activity would be helpful.

DLN Page 3 – Coding DNA Sequence  Stop at the stop codon – It’s painted red  Check whether amino acids match D. melanogaster  Don’t get confused by BLASTX track (ends before stop codon – does not an amino acid) and RNA-seq track (ends after stop codon – 3’UTR)  Final CDS Coordinates are now collected in the yellow boxes

DLN Page 4 – Project Report  DLN Page 3 coordinates in yellow boxes can be used to run the gene model checker  All groups finished a single isoform of one gene on their own in ~15 hours of class time  Honors students completely finished a project during the summer

Constraints/Comments/Collaboration  Lab time to work on new projects is precious. Students can (should?!) complete the example RpS3A annotation on their own by following the instructions and watching the videos.  Shared projects = peer instruction = work through student misconceptions on own to some extent  Digital Laboratory Notebook  Online doc? Google docs/Office 365  Example gene – simple two exon gene (RpS3A or challenging tra (goes with gene intro)  Make the pages like an online form? – pull down menus with limited options instead of free response  Less data entry? Remove repeat track; less gene record finder analysis  Pre-selected projects and pre-formatted notebook pages?

CURE (course-based undergraduate research experience) Achieved  Questions?  Contact Information Nick Reeves Mt. San Jacinto College